I have an Enterprise Manager 13.1 system that is regularly reset to a ‘clean’ state using zfs snapshots. If you already have the management agents installed on other hosts you have the choice of

De-installing the existing agent and installing a clean one

Persuading the agent to talk to your ‘new’ server

A way of doing 2) is to follow the steps outlined in the MOS note EM 12c : Redirecting Oracle Management Agent to Another Oracle Management Service (Doc ID 1390717.1) which despite being for 12c appears to work for Enterprise Manager 13.

Very rarely you can encounter this problem in enterprise manager – a host or agent target that you cannot remove via the web interface. This is usually caused in my environment by decommissioning a host BEFORE the targets have all been dropped (Basically being a gungho dumbass and not considering things properly).

You can do a lot of operations by the emcli command line interface from your enterprise manager host